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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 0
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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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) 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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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) 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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ), 'gf_id' => 'HOM05D001200', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001200' ), 'data_identifier' => 'HOM05D001200', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001200', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '521', 'num_species' => '57' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31LG5G21700' => 'aar', 'AL9U11952' => 'aly', 'AL9U11954' => 'aly', 'arahy.Tifrunner.gnm1.ann1.2QK9Z7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.474EIA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VL02K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9I8ZI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D1ZPVC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DP5I98' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FIPJ9G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UFS61Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.USFH3V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V71EA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WH1VZM' => 'arhy', 'AT2G07633' => 'ath', 'ATCG01060' => 'ath', 'ATCG01070' => 'ath', 'BcaC03g16699' => 'bca', 'BolC2t08908H' => 'bol', 'BolC2t10594H' => 'bol', 'BolC2t10595H' => 'bol', 'BolC2t10596H' => 'bol', 'BolC2t10611H' => 'bol', 'BolC6t36203H' => 'bol', 'BolC6t36208H' => 'bol', 'BolC6t36211H' => 'bol', 'BolC7t43854H' => 'bol', 'BolC7t43855H' => 'bol', 'BolC9t55377H' => 'bol', 'BolC9t56806H' => 'bol', 'BolC9t56807H' => 'bol', 'BolC9t56923H' => 'bol', 'BolC9t56924H' => 'bol', 'BolC9t56925H' => 'bol', 'BolC9t56926H' => 'bol', 'BolC9t56927H' => 'bol', 'BolSC29t60504H' => 'bol', 'BolSC29t60505H' => 'bol', 'BolSC29t60506H' => 'bol', 'BolSC29t60544H' => 'bol', 'BolSC29t60545H' => 'bol', 'BolSC29t60546H' => 'bol', 'BolSC29t60621H' => 'bol', 'BolSC35t60692H' => 'bol', 'BolSC35t60693H' => 'bol', 'BolSC35t60694H' => 'bol', 'BolSC35t60702H' => 'bol', 'BolSC35t60703H' => 'bol', 'BolSC35t60704H' => 'bol', 'BolSC37t60791H' => 'bol', 'BolSC37t60792H' => 'bol', 'BolSC37t60793H' => 'bol', 'BolSC43t60807H' => 'bol', 'BolSC44t60820H' => 'bol', 'BolSC44t60821H' => 'bol', 'BolSC44t60822H' => 'bol', 'BolSC45t60909H' => 'bol', 'BolSC45t60910H' => 'bol', 'BolSC45t60911H' => 'bol', 'BolSC46t60958H' => 'bol', 'BolSC46t60959H' => 'bol', 'BolSC46t60960H' => 'bol', 'BolSC47t61065H' => 'bol', 'BolSC47t61066H' => 'bol', 'BolSC49t61141H' => 'bol', 'BolSC49t61142H' => 'bol', 'BolSC49t61143H' => 'bol', 'BraA10t43432Z' => 'bra', 'BraSC103t45427Z' => 'bra', 'BraSC103t45428Z' => 'bra', 'BraSC103t45429Z' => 'bra', 'BraSC138t45535Z' => 'bra', 'BraSC138t45536Z' => 'bra', 'BraSC143t45660Z' => 'bra', 'BraSC143t45661Z' => 'bra', 'BraSC143t45662Z' => 'bra', 'BraSC179t45774Z' => 'bra', 'BraSC179t45775Z' => 'bra', 'BraSC179t45776Z' => 'bra', 'BraSC25t45908Z' => 'bra', 'BraSC25t45909Z' => 'bra', 'BraSC25t45910Z' => 'bra', 'BraSC58t46460Z' => 'bra', 'BraSC59t46528Z' => 'bra', 'BraSC59t46549Z' => 'bra', 'BraSC59t46550Z' => 'bra', 'BraSC59t46551Z' => 'bra', 'C02p52240' => 'bna', 'C04p22670' => 'bna', 'C06p42250' => 'bna', 'C06p42260' => 'bna', 'C07p33430' => 'bna', 'C07p33440' => 'bna', 'C07p33450' => 'bna', 'C09p24620' => 'bna', 'C09p24630' => 'bna', 'C09p24640' => 'bna', 'C09p39280' => 'bna', 'C09p40190' => 'bna', 'C09p40200' => 'bna', 'C09p40340' => 'bna', 'C09p40350' => 'bna', 'C09p40360' => 'bna', 'C09p40370' => 'bna', 'CAN.G100.34' => 'can', 'CAN.G108.6' => 'can', 'CAN.G127.8' => 'can', 'CAN.G1526.3' => 'can', 'CAN.G1526.7' => 'can', 'CAN.G1526.8' => 'can', 'CAN.G278.3' => 'can', 'CAN.G278.4' => 'can', 'CAN.G386.25' => 'can', 'CAN.G8.22' => 'can', 'CAN.G904.13' => 'can', 'CAN.G95.10' => 'can', 'CAN.G965.6' => 'can', 'CAN.G965.7' => 'can', 'CARHR258570' => 'chi', 'CARHR282420' => 'chi', 'CARHR282430' => 'chi', 'CARHR282440' => 'chi', 'Ciclev10006660m.g' => 'ccl', 'Ciclev10010880m.g' => 'ccl', 'Ciclev10013969m.g' => 'ccl', 'Ciclev10013970m.g' => 'ccl', 'Ciclev10013974m.g' => 'ccl', 'Ciclev10013975m.g' => 'ccl', 'Ciclev10027631m.g' => 'ccl', 'Ciclev10027632m.g' => 'ccl', 'Ciclev10027650m.g' => 'ccl', 'Ciclev10027651m.g' => 'ccl', 'Ciclev10030458m.g' => 'ccl', 'Ciclev10030459m.g' => 'ccl', 'CiPaw.16G059700' => 'cil', 'ClCG00G001520' => 'cla', 'Cpa.g.sc63.22' => 'cpa', 'CsaV3_6G032290' => 'csa', 'CsaV3_UNG210140' => 'csa', 'CsaV3_UNG210150' => 'csa', 'CSS0005564' => 'camsi', 'CSS0038532' => 'camsi', 'DCAR_025284' => 'dca', 'DCAR_032536' => 'dca', 'DCAR_032537' => 'dca', 'DCAR_032538' => 'dca', 'EL10As15g24099' => 'bvu', 'EL10As15g24100' => 'bvu', 'EL10As15g24137' => 'bvu', 'Eucgr.L00013' => 'egr', 'Glyma.08G367600' => 'gma', 'Glyma.18G155300' => 'gma', 'Glyma.18G155400' => 'gma', 'Gohir.1Z049531' => 'ghi', 'Gohir.1Z049631' => 'ghi', 'Gohir.1Z049731' => 'ghi', 'Gohir.A01G112200' => 'ghi', 'Gohir.A01G139671' => 'ghi', 'Gohir.A01G143400' => 'ghi', 'Gohir.A02G134201' => 'ghi', 'Gohir.A02G134400' => 'ghi', 'Gohir.A02G134500' => 'ghi', 'Gohir.A04G053130' => 'ghi', 'Gohir.A08G113700' => 'ghi', 'Gohir.A09G017925' => 'ghi', 'Gohir.A09G040995' => 'ghi', 'Gohir.A09G046200' => 'ghi', 'Gohir.A13G109925' => 'ghi', 'Gohir.D03G063001' => 'ghi', 'Gohir.D04G175000' => 'ghi', 'Gohir.D06G133600' => 'ghi', 'Gohir.D08G035150' => 'ghi', 'Gohir.D08G077250' => 'ghi', 'Gohir.D13G018850' => 'ghi', 'Gohir.D13G164800' => 'ghi', 'Gorai.004G033100' => 'gra', 'Gorai.004G082100' => 'gra', 'Gorai.006G071400' => 'gra', 'Gorai.009G377500' => 'gra', 'Gorai.012G007400' => 'gra', 'Gorai.013G020900' => 'gra', 'Gorai.013G108500' => 'gra', 'GSVIVG01004976001' => 'vvi', 'GSVIVG01016016001' => 'vvi', 'GSVIVG01023756001' => 'vvi', 'GSVIVG01023765001' => 'vvi', 'GSVIVG01023768001' => 'vvi', 'GSVIVG01034636001' => 'vvi', 'HanXRQChr00c0196g0572481' => 'han', 'HanXRQChr00c0289g0573121' => 'han', 'HanXRQChr00c0289g0573131' => 'han', 'HanXRQChr00c0328g0573601' => 'han', 'HanXRQChr00c0328g0573611' => 'han', 'HanXRQChr00c0336g0573651' => 'han', 'HanXRQChr00c0336g0573661' => 'han', 'HanXRQChr00c0504g0575301' => 'han', 'HanXRQChr00c0690g0576761' => 'han', 'HanXRQChr00c0703g0576951' => 'han', 'HanXRQChr00c0894g0577811' => 'han', 'HanXRQChr01g0000241' => 'han', 'HanXRQChr01g0020071' => 'han', 'HanXRQChr02g0038661' => 'han', 'HanXRQChr02g0038671' => 'han', 'HanXRQChr02g0038701' => 'han', 'HanXRQChr02g0038711' => 'han', 'HanXRQChr02g0040741' => 'han', 'HanXRQChr02g0059711' => 'han', 'HanXRQChr03g0073091' => 'han', 'HanXRQChr03g0073101' => 'han', 'HanXRQChr05g0152431' => 'han', 'HanXRQChr05g0152441' => 'han', 'HanXRQChr06g0183001' => 'han', 'HanXRQChr07g0204721' => 'han', 'HanXRQChr08g0211961' => 'han', 'HanXRQChr08g0211971' => 'han', 'HanXRQChr08g0211981' => 'han', 'HanXRQChr08g0213671' => 'han', 'HanXRQChr08g0231311' => 'han', 'HanXRQChr09g0244731' => 'han', 'HanXRQChr09g0246671' => 'han', 'HanXRQChr09g0246681' => 'han', 'HanXRQChr09g0258511' => 'han', 'HanXRQChr09g0258521' => 'han', 'HanXRQChr10g0289681' => 'han', 'HanXRQChr11g0323741' => 'han', 'HanXRQChr11g0323751' => 'han', 'HanXRQChr12g0383551' => 'han', 'HanXRQChr13g0388461' => 'han', 'HanXRQChr13g0393091' => 'han', 'HanXRQChr14g0428461' => 'han', 'HanXRQChr15g0465441' => 'han', 'HanXRQChr15g0465451' => 'han', 'HanXRQChr17g0557751' => 'han', 'HanXRQChr17g0557761' => 'han', 'HanXRQChr17g0557771' => 'han', 'HanXRQChr17g0569731' => 'han', 'HanXRQChr17g0569741' => 'han', 'HanXRQCPg0580351' => 'han', 'Hma1.2p1_0382F.1_g140210' => 'hma', 'Hma1.2p1_0656F.1_g196803' => 'hma', 'Hund03917' => 'sun', 'Hund03918' => 'sun', 'Hund08792' => 'sun', 'Hund08793' => 'sun', 'Hund10653' => 'sun', 'Hund12715' => 'sun', 'Hund12716' => 'sun', 'Hund12842' => 'sun', 'Hund12843' => 'sun', 'Hund23967' => 'sun', 'Hund23968' => 'sun', 'Hund24329' => 'sun', 'Hund27630' => 'sun', 'Hund27631' => 'sun', 'Hund27632' => 'sun', 'Hund27678' => 'sun', 'Hund27679' => 'sun', 'Hund27755' => 'sun', 'Hund27756' => 'sun', 'Hund27831' => 'sun', 'Hund27832' => 'sun', 'Hund27883' => 'sun', 'Hund28330' => 'sun', 'Hund28331' => 'sun', 'Hund28438' => 'sun', 'Hund28439' => 'sun', 'Hund28447' => 'sun', 'Hund28448' => 'sun', 'Hund28536' => 'sun', 'Hund28537' => 'sun', 'Hund28586' => 'sun', 'Hund28587' => 'sun', 'Hund28595' => 'sun', 'Hund28596' => 'sun', 'Hund28597' => 'sun', 'Hund28613' => 'sun', 'Hund28849' => 'sun', 'Hund28850' => 'sun', 'Hund28851' => 'sun', 'Hund28880' => 'sun', 'Hund28937' => 'sun', 'Hund28945' => 'sun', 'Hund28946' => 'sun', 'Hund28950' => 'sun', 'Hund28951' => 'sun', 'Hund28954' => 'sun', 'Hund28955' => 'sun', 'Hund28960' => 'sun', 'Hund28961' => 'sun', 'Hund28973' => 'sun', 'Hund28974' => 'sun', 'Hund28979' => 'sun', 'Hund28980' => 'sun', 'Hund29026' => 'sun', 'Hund29027' => 'sun', 'Hund29089' => 'sun', 'Hund29090' => 'sun', 'Hund29108' => 'sun', 'Hund29109' => 'sun', 'Hund29179' => 'sun', 'Hund29180' => 'sun', 'Hund29185' => 'sun', 'Hund29186' => 'sun', 'Hund29243' => 'sun', 'Hund29244' => 'sun', 'Hund29247' => 'sun', 'Hund29248' => 'sun', 'Hund29250' => 'sun', 'Hund29251' => 'sun', 'Hund29254' => 'sun', 'Hund29255' => 'sun', 'Hund29261' => 'sun', 'Hund29262' => 'sun', 'Hund29272' => 'sun', 'Hund29273' => 'sun', 'Hund29276' => 'sun', 'Hund29277' => 'sun', 'Hund29280' => 'sun', 'Hund29281' => 'sun', 'Hund29284' => 'sun', 'Hund29285' => 'sun', 'Hund29288' => 'sun', 'Hund29289' => 'sun', 'Hund29316' => 'sun', 'Hund29317' => 'sun', 'Hund29433' => 'sun', 'Hund29434' => 'sun', 'Hund29435' => 'sun', 'Hund29437' => 'sun', 'Hund29438' => 'sun', 'Hund29452' => 'sun', 'Hund29453' => 'sun', 'Hund29498' => 'sun', 'Hund29499' => 'sun', 'Hund29653' => 'sun', 'Hund29654' => 'sun', 'Hund29713' => 'sun', 'Hund29714' => 'sun', 'Hund29755' => 'sun', 'Hund29756' => 'sun', 'Hund29813' => 'sun', 'Hund29814' => 'sun', 'Hund29817' => 'sun', 'Hund29818' => 'sun', 'Hund30036' => 'sun', 'Hund30037' => 'sun', 'Hund30038' => 'sun', 'Hund30039' => 'sun', 'Hund30120' => 'sun', 'Hund30121' => 'sun', 'Hund30177' => 'sun', 'Hund30178' => 'sun', 'Hund30365' => 'sun', 'Hund30388' => 'sun', 'Hund30513' => 'sun', 'Hund30643' => 'sun', 'Lalb_Chr07g0191751' => 'lal', 'Lalb_Chr07g0191761' => 'lal', 'Lalb_Chr07g0191771' => 'lal', 'Lalb_Chr13g0292801' => 'lal', 'Lalb_Chr13g0292811' => 'lal', 'Lalb_Chr13g0292821' => 'lal', 'Lalb_Chr13g0292831' => 'lal', 'Lalb_Chr16g0388551' => 'lal', 'Lalb_Chr18g0049421' => 'lal', 'Lalb_Chr18g0049431' => 'lal', 'Lalb_Chr18g0049441' => 'lal', 'Lalb_Chr19g0127741' => 'lal', 'Lalb_Chr19g0127811' => 'lal', 'Lalb_Chr23g0274791' => 'lal', 'Lj2g0021700' => 'lja', 'Lj2P1238T97' => 'lonja', 'LjContig00318g0024402' => 'lja', 'LjContig00319g0019579' => 'lja', 'Lsat_1_v5_gn_1_14180' => 'lsa', 'Lsat_1_v5_gn_1_14200' => 'lsa', 'Lsat_1_v5_gn_6_54081' => 'lsa', 'Lsat_1_v5_gn_6_54101' => 'lsa', 'Manes.17G012600' => 'mes', 'Mapoly0012s0041' => 'mpo', 'Mapoly0092s0003' => 'mpo', 'MBI10_g47590_MAGBIO' => 'mbi', 'MBI10_g47593_MAGBIO' => 'mbi', 'MBI16_g21734_MAGBIO' => 'mbi', 'MD04G1189100' => 'mdo', 'Medtr0002s0170' => 'mtr', 'Medtr0148s0110' => 'mtr', 'Medtr1g040655' => 'mtr', 'Medtr1g081540' => 'mtr', 'Medtr1g085100' => 'mtr', 'Medtr1g085110' => 'mtr', 'Medtr1g103000' => 'mtr', 'Medtr2g042860' => 'mtr', 'Medtr2g047260' => 'mtr', 'Medtr2g048620' => 'mtr', 'Medtr2g102090' => 'mtr', 'Medtr2g103350' => 'mtr', 'Medtr3g008330' => 'mtr', 'Medtr3g071600' => 'mtr', 'Medtr3g073110' => 'mtr', 'Medtr3g082380' => 'mtr', 'Medtr3g109440' => 'mtr', 'Medtr3g114440' => 'mtr', 'Medtr4g006120' => 'mtr', 'Medtr4g026420' => 'mtr', 'Medtr4g050950' => 'mtr', 'Medtr4g050960' => 'mtr', 'Medtr4g080900' => 'mtr', 'Medtr4g086110' => 'mtr', 'Medtr4g106580' => 'mtr', 'Medtr4g128700' => 'mtr', 'Medtr5g021300' => 'mtr', 'Medtr5g032430' => 'mtr', 'Medtr5g089040' => 'mtr', 'Medtr5g094180' => 'mtr', 'Medtr5g099080' => 'mtr', 'Medtr5g464700' => 'mtr', 'Medtr6g080310' => 'mtr', 'Medtr7g012690' => 'mtr', 'Medtr7g021720' => 'mtr', 'Medtr7g044990' => 'mtr', 'Medtr7g045000' => 'mtr', 'Medtr7g086590' => 'mtr', 'Medtr7g108460' => 'mtr', 'Medtr7g112630' => 'mtr', 'Medtr8g056200' => 'mtr', 'Medtr8g085370' => 'mtr', 'Medtr8g086440' => 'mtr', 'Medtr8g087010' => 'mtr', 'MELO3C027236.2' => 'cme', 'MELO3C029829.2' => 'cme', 'Migut.D01252' => 'egut', 'Migut.D01253' => 'egut', 'Migut.D01254' => 'egut', 'Migut.D01255' => 'egut', 'Migut.D01384' => 'egut', 'Migut.D01520' => 'egut', 'Nitab4.5_0001313g0070' => 'nta', 'Nitab4.5_0001342g0130' => 'nta', 'Nitab4.5_0002738g0110' => 'nta', 'Nitab4.5_0002738g0120' => 'nta', 'Nitab4.5_0007979g0060' => 'nta', 'Nitab4.5_0010611g0010' => 'nta', 'Nn031s41613' => 'nnu', 'Nn064s42210' => 'nnu', 'Nn064s42211' => 'nnu', 'Nn064s42212' => 'nnu', 'Nn1g00557' => 'nnu', 'Nn1g00558' => 'nnu', 'Nn1g08634' => 'nnu', 'Nn1g08635' => 'nnu', 'Nn3g19076' => 'nnu', 'Nn3g20216' => 'nnu', 'Nn3g20217' => 'nnu', 'Oeu012765.1' => 'oeu', 'Oeu012819.1' => 'oeu', 'Oeu019750.1' => 'oeu', 'Oeu022126.1' => 'oeu', 'Oeu023788.1' => 'oeu', 'Oeu036838.1' => 'oeu', 'Oeu043656.1' => 'oeu', 'Oeu048498.1' => 'oeu', 'Oeu053979.1' => 'oeu', 'Os09g0485201' => 'osa', 'Peaxi162Scf00030g02118' => 'pax', 'Peaxi162Scf01164g00035' => 'pax', 'PGR111G0008' => 'pgr', 'PGR111G0025' => 'pgr', 'PGSC0003DMG400020539' => 'stu', 'PGSC0003DMG400026713' => 'stu', 'PGSC0003DMG401011339' => 'stu', 'PGSC0003DMG402011339' => 'stu', 'Phvul.002G050301' => 'pvu', 'Phvul.011G095700' => 'pvu', 'Potri.008G202133' => 'ptr', 'Potri.019G014344' => 'ptr', 'Pp3c2_10430' => 'ppa', 'PSO548G0036' => 'pso', 'PSO548G0037' => 'pso', 'RcHm_v2.0_Chr5g0017211' => 'rch', 'RcHm_v2.0_Chr5g0017221' => 'rch', 'RcHm_v2.0_Chr5g0017231' => 'rch', 'RcHm_v2.0_Chr5g0043031' => 'rch', 'RcHm_v2.0_Chr5g0043041' => 'rch', 'RcHm_v2.0_Chr5g0043051' => 'rch', 'RcHm_v2.0_CPg0502771' => 'rch', 'RcHm_v2.0_CPg0502781' => 'rch', 'RcHm_v2.0_CPg0502791' => 'rch', 'RcHm_v2.0_CPg0502801' => 'rch', 'RcHm_v2.0_CPg0502811' => 'rch', 'SalBow1G7634' => 'sbo', 'SalBow2G1265' => 'sbo', 'Sed0012006' => 'sed', 'Sed0012820' => 'sed', 'Sed0023939' => 'sed', 'SEGI_13011' => 'sgi', 'SEGI_22361' => 'sgi', 'SMO086G0019' => 'smo', 'SMO086G0020' => 'smo', 'SMO086G0058' => 'smo', 'Solyc01g065585.1' => 'sly', 'Solyc01g065610.1' => 'sly', 'Solyc01g065620.1' => 'sly', 'Solyc01g065630.1' => 'sly', 'Solyc01g065640.3' => 'sly', 'Solyc02g011740.1' => 'sly', 'Solyc02g011750.1' => 'sly', 'Solyc02g011760.1' => 'sly', 'Solyc10g047420.3' => 'sly', 'Solyc11g021213.1' => 'sly', 'Solyc11g021215.1' => 'sly', 'Solyc11g044600.2' => 'sly', 'Solyc11g044647.1' => 'sly', 'Sp1g31800' => 'spa', 'Thhalv10017742m.g' => 'esa', 'TPR.G17270' => 'tpr', 'TPR.G24765' => 'tpr', 'TPR.G24771' => 'tpr', 'TPR.G28924' => 'tpr', 'TPR.G30364' => 'tpr', 'TPR.G7852' => 'tpr' ) $gf_id = 'HOM05D001200' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001200' ) $data_identifier = 'HOM05D001200' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aly' => (int) 2, 'arhy' => (int) 11, 'ath' => (int) 3, 'bca' => (int) 1, 'bol' => (int) 49, 'bra' => (int) 20, 'bna' => (int) 17, 'can' => (int) 14, 'chi' => (int) 4, 'ccl' => (int) 12, 'cil' => (int) 1, 'cla' => (int) 1, 'cpa' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 2, 'dca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 1, 'gma' => (int) 3, 'ghi' => (int) 22, 'gra' => (int) 7, 'vvi' => (int) 6, 'han' => (int) 50, 'hma' => (int) 2, 'sun' => (int) 116, 'lal' => (int) 14, 'lja' => (int) 3, 'lonja' => (int) 1, 'lsa' => (int) 4, 'mes' => (int) 1, 'mpo' => (int) 2, 'mbi' => (int) 3, 'mdo' => (int) 1, 'mtr' => (int) 44, 'cme' => (int) 2, 'egut' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 1, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 1, 'pso' => (int) 2, 'rch' => (int) 11, 'sbo' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 13, 'spa' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 6 ) $gf_gene_species = 'tpr' $gf_gene_id = 'TPR.G7852' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 0